Note: Descriptions are shown in the official language in which they were submitted.
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Title: Methods for labeling nucleotides, labeled
nucleotides and useful intermediates.
The invention relates to methods for labeling nucleotides
using linkers (linking moieties between labels and bio-organic
molecules, which linkers are based on platinum compounds).
Platinum (coordination) compounds have been considered
interesting molecules for a very long time. For a review of
these compounds and their uses we refer to Reedijk et al.
(Structure and Bonding 67, p.53-89, 1987). Especially Cis-
platinum has received a lot of attention as a possible anti-
tumour drug. This anti-tumour reactivity of platinum compounds
originates from their having at least two reactive groups
(preferably cis-oriented towards each other), which make it
possible to cross-link DNA molecules, thereby inhibiting the
replication of these DNA molecules.
The British patent application 2 148 891 discloses cis-
platinum complexes, which are six-coordinated. The platinum is
attached to two halogens or hydroxy groups, two additional
halogens and to an ethylene diamine derived group, such as
1,2-diamino-2-methylpropane or 1,2-diamino-2-methylbutane. The
complexes are said to have an excellent anti-tumor effect.
In the European patent application four-coordinated
complexes of platinum to 2,3-alkyl-1,4-butanediamine and two
halogens are described for their anti-tumor effect.
Different four-coordinated platinum complexes are
described in the European patent application 0 386 243. The
complexes comprise a diamine bidentate ligand and two 2-
arylalkanoic acid or 3-aryl-2-oxoalkanoic acid ligands. These
complexes are stated to have a strong growth inhibiting action
on certain leukemia cells and are used for their oncostatic
activity.
US patent 4,207,416 discloses ethylenediamine-
platinum(II) 2,4-dioxopyrimidine complexes as having a high
anti-tumor activity and low mammalian toxicity.
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A different use of platinum (coordination) compounds has
been disclosed in PCT application (W092/01699) wherein a
platinum compound having only two reactive moieties
(denominated as leaving groups therein) is reacted with a
fluorescein to obtain a labeled platinum compound which can
bind (non-covalently) to a nucleic acid, preferably at the N-7
position of a guanine residue.
Several methods for labeling nucleotides have been
described in the literature. For a long time, the standard
method has been to use radioactive isotope labeling. However,
there are a number of problems associated with the use of
radioisotopes, such as potential health hazards, disposal
problems and instability problems.
In order to overcome these problems, Dale et al.,
Biochemistry, 14, (1975), 2447-2457, have proposed to use
direct covalent mercuration as a labeling technique for
nucleotides and polynucleotides. It was found, that cytosine
and uracil may be mercurated at their C5-position under mild
conditions. Further, Gebeyehu et al., Nucleic Acids Research,
15, (1987), 4513-4534, have reported that adenine and cytosine
may be labeled with biotin derivatives through an aliphatic
linker of from 3 to 17 atoms.
A major drawback of these known methods is that they are
not suitable for labeling all different nucleotides. For
instance, Dale et al. reported that their covalent mercuration
method leads to negative results for adenine, thymine and
guanine bases. In some cases, for example when only a few
residues of a certain nucleotide are present in a certain
nucleic acid or when the terminating nucleotide residue of a
nucleic acid has to be labeled, it is desired to have at one's
disposal a method for labeling any nucleotide residue.
The present invention provides such a method. The method
for labeling nucleotides of the invention comprises the steps
of
- reacting a reactive moiety of a linker of the formula
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X
Pt
(I)
A B
wherein X represents any stabilizing bridge and wherein A
and B represent the same or different reactive moieties,
with an electron donating moiety of a spacer, which spacer
comprises a chain having at least four atoms and at least
one heteroatom in the chain, which spacer further comprises
said electron donating moiety at one end of the chain and a
reactive moiety at the other end of the chain;
- reacting the reactive moiety of said spacer with a label;
- reacting the other reactive moiety of said linker with a
nucleotide.
According to the invention, the linker may first be
attached to the nucleotide and then to the spacer, or vice
versa and the spacer may first be coupled to the label and
then to the linker or vice versa.
The reactive moiety of the spacer may be any reactive
moiety that will enable the reaction between the spacer and
the label in such a manner that a labeling moiety comrpising a
label and a spacer is formed, which labeling moiety is
sufficiently stable.
The main purpose for labeling nucleotides is that these
labeled nucleotides can be incorporated in nucleic acid
molecules. Modified nucleotides, especially those wherein a
(bulky) label is attached to the nucleotide, are often built-
in into nucleic acids with a much lower efficiency. The
methods according to the invention result in labeled
nucleotides which are built-in into nucleic acids with a
higher efficiency than the labeled nucleotides available to
date. This is probably for due to the selection of the spacers
according to the invention in combination with the platinum-
based linkers according to the invention.
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The label to be used according to the invention is not
critical. In principle all labels which can be attached to a
nucleotide and are employed to date can be used. These labels
may be radioactive labels, enzymes (which need reaction with a
substrate to be detected), specific binding pairs components
such as avidin, streptavidin or biotin, biocytin, iminobiotin,
colloidal dye substances, fluorochromes (rhodamin, etc.),
reducing substances (eosin, erythrosin, etc.), (coloured)
latex sols, digoxigenin, metals (ruthenium), metal sots or
other particulate sols (selenium, carbon and the like), dansyl
lysin, Infra Red Dyes, coumarines (amino methyl coumarine),
antibodies, protein A, protein G, etc. The invention has most
benefits with bulkier labels such as biotin, avidin,
streptavidin, digoxygenin or a functional equivalent thereof.
The invention is not limited to nucleotides or
nucleosides as such; derivatives and functional equivalents
are also included. The usual nucleotides adenine, thymidine,
cytosine, guanine and uridine are preferred. Especially the
purines are preferred which have a very good incorporation
rate.
For coupling of the spacer to the platinum linker an
electron donating moiety is required. In a preferred method
the electron donating moiety is an amine or a thiolate anion,
which have both proven to be very succesful. It was found that
aromatic amines, such as imidazoles or purines, are capable of
forming very strong bonds to platinum and thus are very
suitable for use as the electron donating moiety.
The spacer is an important aspect of the present
invention; it provides the easiest coupling between label and
linker. For avoiding steric hindrance in incorporation of the
nucleotide into the nucleic acid it should at least be four
atoms long, preferably it is at least four carbon atoms long
and has at least one heteroatom in that carbon chain. A
heteroatom confers a certain amount of rigidity on the spacer.
This rigidity provides an additional assurance that steric
factors will not obstruct a convenient linking of a nucleotide
and a label. It is preferred that at least one heteroatom is
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an oxygen atom, which positively effects the hydrophilicity of
the spacer.
Preferably, the spacer comprises no more than 20 carbon
atoms in the chain, which is preferably an essentially non-
5 branched chain, thus causing no steric hindrance. The reason
for this will be clear.
A highly preferred spacer is 1,8-diamino-3,6-dioxaoctane,
herein referred to as Dadoo. Dadoo is a very flexible compound
with a distal primary amine group and a size that makes it
very suitable for use as spacer according to the invention.
Another highly preferred spacer of the invention is an
oligolysine or a polylysine. Due to their structure and
conformation, these molecules create the most convenient
environment for an optimal interaction among the actual label,
the nucelotide and the platinum. An additional advantage of
the use of lysine chains as the spacer is, that by altering
the number of lysine units in the chain, the optimal
conditions for specific labels and nucleotides or nucleic
acids can be attained. Given a certain application, the
skilled person will easily determine how many lysine units are
required for optimum results.
An especially interesting labeling moiety comprising a
label and a spacer, has the formula
NH2 - (CH2)n -NH2
X Pt
(II)
label
or the formula
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Z NH2 - ( CH 2 )n -NH2
Pt
(III)
label Z'
wherein X represents any stabilizing bridge, Z and Z'
represent a non-leaving ligand and n is an integer of from 2
to 10.
Accordingly, the linker-spacer-label-system, or labeling
substance, with the labeling moiety of formula (II) or formula
(III) has the formula
X X
Pt ~ Pt
(IV)
A H2N_(CH2)n_Ng2 label
or the formula
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X
Z label
Pt ~ Pt
A~ ~ N-(CH ) -NH ~ (
2 2 n
wherein A, X, Z, Z' and n have the above meanings.
The non-leaving ligands Z and/or Z' are preferably an
NH3, NH2R, NHR2 or NR3 group, wherein R represents an alkyl
group having from 1 to 6 carbon atoms, because these ligands
have an even smaller leaving-group character than other non-
leaving ligands.
The interesting feature of using the labeling moieties
having formulas (II) and (III) is that both the nucleotide and
the actual label have the benefit of being bonded directly to
a platinum atom, while at the same time these moieties are
sufficiently far apart to avoid steric hindrance.
The linkers according to the invention preferably are
platinum compounds wherein X represents an aliphatic diamine.
In a preferred embodiment of the invention, one or both of the
nitrogen atoms of the aliphatic diamine are shielded. A
suitable manner of shielding these nitrogen atoms consists of
substitution with one or two alkyl groups of from 1 to 6
carbon atoms, preferably methyl groups. This is advantageous
in that hydrogen bonding between the triphosphate group of a
nucleotide and the stabilizing bridge is prevented.
Preferably, a diamine having 2-6 carbon atoms is used, most
preferably an ethylene diamine group, which is well-known for
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its stabilizing effect on this class of platinum compounds. In
this case, the linker has the formula
H2C CH2
G2N ~ / NG2
Pt
(VI)
A B
wherein G represents hydrogen or an alkyl group of from 1 to 6
carbon atoms and A and B represent the same or different
reactive moieties.
The coupling or reactive moieties A and B are preferably
the same and selected from the group consisting of N03-, S03-
Cl-, I-, or other halogens.
The invention of course also encompasses a labeled
nucleotide obtainable by a method as disclosed above.
In addition, the invention encompasses a labeling
substance for labeling nucleotides by a method as disclosed
above. The labeling substance of the invention has the formula
X
Pt
(VII)
A labeling
moiety
wherein X and A have the above meanings and the labeling
moiety comprises a label and a spacer as described above. Of
course the labeling substances of the invention can also be
used for labeling purposes other than labeling nucleotides. It
was found that numerous (bio-) organic compounds, i.e. nearly
every bio-organic molecule which contains an accessible
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sulphur or nitrogen atom, for example proteins, can be labeled
with the platinum compounds of the invention.
A great advantage of the invention arises from the use of
the platinum compounds having formula (I) as linkers in the
methods of preparing labeled nucleotides according to the
invention. These linkers can be prepared by very convenient
and reliable methods.
In W092/01699 the starting compounds disclosed for
preparing labeled platinum compounds are
platinum(II)(ethylenediamine)dichloride and
platinum(II)(ethylenediamine)(Me2S0)Cl. The first one can be
obtained commercially, the second one (the preferred one) must
be synthesized. In the dichloride compound, the Cl-ions are
less readily substituted by a label or a nucleotide,
respectively. In the latter case, the total nucleotide
labeling time will be appreciably longer, up to several hours,
instead of several minutes.
The methods for preparing the linkers that are used in
the method of labeling nucleotides according to the invention
are based on the selection of suitable starting compounds of
the formula PtE4 wherein E is an electronegative group,
preferably a halogen or N03- or S03-. The reaction, which is
described in the examples, of these starting compounds with
e.g. ethylenediamine is very simple and efficient. Moreover,
this reaction leads to very suitable symmetric intermediate
compounds for producing labeled nucleotides. A major advantage
of using these compounds is that when a stabilizing bridge for
the resulting platinum compound has to be attached that no
blocking reagents have to be employed. Another advantage is
that the resulting intermediate compounds can again be labeled
without the use of blocking agents. Therefore steps removing
blocking agents can be eliminated completely. Furthermore the
yields of these reactions are very high. Yet another advantage
of the use of these symmetrical starting compounds is that no
mixtures of different resulting compounds can be formed, which
may interfere with the following reaction and reduce yield or
require extra separation steps.
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A very suitable intermediate compound according to the
invention is platinum(II)(ethylenediamine)(N03)2. This
substance can very easily be provided with a suitable spacer
and a labeling group, resulting in labeling substances which
5 can, through substitution of the remaining N03-group be linked
to a nucleotide quite easily. Furthermore the methods for
producing these compounds and the resulting compounds do not
involve highly toxic substances such as DMSO.
The intermediate compounds can be labeled with any
10 suitable label (also known as marker) through a spacer as
disclosed hereinabove.
Furthermore, the known advantages (from W092/01699 for
instance) are of course also obtained with the present methods
and compounds. Another advantage of the platinum compounds is
that they can be detected more or less directly by using the
platinum as a nucleus for depositing silver or other metal
crystals.
By binding the labeling substance to a nucleotide
residue, DNA or RNA molecules, be it single stranded or
otherwise, can be easily detected, but it also allows for the
production of probes for hybridization techniques wherein
unlabeled DNA/RNA molecules hybridize to the labeled probe.
The platinum linker labeled nucleotides do hardly interfere
with the hybridization, if at all. Also, this technique
obviates the use of modified nucleotides in preparing probes.
Nucleotides modified in accordance with the practices of
this invention and oligo- and polynucleotides into which the
modified nucleotides have been incorporated or oligo- and
polynucleotides that have been directly modified using these
novel platinum compounds may be used as probes in biomedical
research, clinical diagnostics and recombinant DNA technology.
Other advantages and embodiments of the invention will
become clear from the following experimental part and the
examples.
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EXPERIMENTAL
SYNTHESIS OF INTERMEDIATE PLATINUM COMPOUNDS
These compounds, i.e. the linkers having formula (I), may
be prepared by a process which involves:
(a) reacting a,compound having the structure:
C1 C1
Pt
C1 Cl
with KI in a suitable solvent under suitable conditions so as
to form a iodated platinum compound having the structure:
I I
Pt
I T
(b) reacting said iodated platinum compound with
ethylenediamine in a suitable solvent so as to form a
diethyleneamine iodated platinum compound and represented by
the formula Pt(en)I2 and having the structure:
H2N- ~ NH2
\\Pt
I I
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(c) reacting said compound with AgNO3, the reaction being
carried out in a suitable solvent, under suitable conditions
so as to form a compound having the structure:
H2N \ ~NH2
Pt
03N N03
(d) reacting said compound with KCl in a suitable solvent
under suitable conditions so as to form a compound having the
structure:
H2N- ~ NH2
\\Pt
C1 C1
(e} reacting said compound with AgN03 in a suitable solvent,
under suitable conditions so as to form a compound having the
structure:
H2N \ / NH2
Pt
03N N03
(f) recovering said compound as modified platinum starting
compound for the synthesis of hapten-bound Pt(en) compounds
for use as DNA and/or RNA label.
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Example 1
Preparation of Platinumethylenediamine(N03)2: starting
material.
Pt(en)(N03)2
All reactions are performed in the dark
Dissolve 1 gram potassium tetrachloroplatinate (II),
K2PtC14 (2.4 mmol, Sigma) in 50 ml millipore (filtered water)
and stir at room temperature. Add 10 equivalents of potassium
iodide, KI (24 mmol, 3.999 g, Sigma). The colour of the
solution will immediately turn from orange into dark red
(K2PtI4), stir for 5 minutes.
Add one equivalent ethylenediamine (2.4 mmol, 160.8743 ~.1,
Merck 11=0.9 kg) after diluting 161 ~.1 ethylenediamine in 5 ml
millipore very slowly to the platinum solution, mix this
solution for 1 hour at room temperature.
A yellow/brown precipitate, Pt(en)I2, will be formed and
the liquid standing above should be clear.
Filter the solution through a 1.0 8.m membrane filter
(Schleicher&Schuell), wash the precipitate with millipore,
ethanol and diether (in this order). Dry the Pt(en)I2 for at
least 4 hours in a vacuum dryoven at 37°C.
Weigh the dried Pt(en)I2 (--1.07 g) and suspend it in 45 ml
millipore/5 ml aceton, the solution will be cloudy. Add 1.95
equivalent of AgN03 (M = 169.9, Sigma). Stir the reaction
overnight at room temperature.
Filter the solution through a 1.0 Eun membrane filter, the
precipitate is Silveriodide, AgI, the filtrate should be
clear.
Add to 0.5 ml of the filtrate, Pt(en)(N03)2, an excess of
KCl or NaCl and make sure that no white precipitate is formed
immediately after adding the excess of KC1 or NaCl. If no
white precipitate (only a yellow one) is formed than add an
excess of KCl or NaCl to the entire filtrate. After the yellow
precipitate is formed filter the solution and wash the
precipitate (Pt(en)C12) with millipore, ethanol and diether.
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Dry the precipitate for at least 4 hours in a vacuum
dryoven at 37°C .
Weigh the dry Pt(en)C1z (M=326,1), and suspend it in 45 ml
millipore/5 ml aceton and stir the cloudy suspension. Add 1.95
equivalent AgN03 and stir the solution overnight at room
temperature. The colour of the solution will become white, due
to the formation of AgCl.
Filter the solution in the dark and evaporate the
filtrate to remove the aceton by rotation evaporation untill
25 ml of the filtrate is left. The filtrate is then
freezedried. The product is checked by NMR or Infrared
Absorption Spectroscopy.
Preparation of Platinum-N,N,N',N'-
tetramethylethylenediamine(N03)2: starting material.
Pt(tmen)(N03)2
All reactions are performed in the dark
Repeat the entire procedure of Example 1A, but use N,N,N',N'-
tetramethylethylenediamine instead of ethylenediamine.
Example 2
A Preparation of fPt(en~tR~~Dadoo-NH~,)fNQ~ll(N0~1
Dissolve Pt(en)(N03)2 (18.2 mg, 0.048 mmol) in 10 ml of
Millipore water and heat until dissolving. Dissolve BioDadoo
(20 mg, 0.053 mmol, purchased from Boehringer Mannheim) in 5
ml of Millipore water. Add the two solutions together and
adjust the pH to 8 by 0.1 N NaOH, react for at least 3 hours
at 50°C. Isolate the end product by freeze drying.
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B. Preparation of fPtltmen L(BioDadoo-NH~~ N0~11(NO~"Z
Dissolve Pt(tmen)(N03)2 (35 mg, 0.08 mmol) in 12.5 ml of
Millipore water and heat until dissolving. Dissolve BioDadoo
5 (32 mg, 0.085 mmol) in 10 ml of Millipore water. Add the two
solutions together and adjust the pH by 0.1 N NaOH, react for
at least 4 hours at 50°C. Isolate the end product by freeze
drying.
10 C . Preparation of f Pt~g~ L,~(~g~Dadoo-NH~,~ NO~~~ 1 ( NO~~
Dissolve Pt(en)(N03)2 (5 mg, 0.013 mmol) in 5 ml of Millipore
water and heat until dissolving. Dissolve DigDadoo (9 mg,
0.016 mmol, purchased from Boehringer Mannheim) in 5 ml of
15 Millipore water. Add the two solutions together and react for
at least 4 hours at 50°C. Isolate the endproduct by freeze
drying.
Example 3
Dissolve [Pt(en)(BioDadoo-NH2)(N03)](N03) (9 mg, 0.012 mmol) in
2 ml of Millipore water. Add 2'-deoxyguanosine-5'-triphosphate
(2.3 mg, 0.004 mmol) and adjust the pH to 6. Incubate for 24
hours at 50°C, freeze-dry and redissolve in Millipore water (1
ml) and filter through a membrane filter. Apply the mixture to
a FPLC with MonoQ and purify with a linear gradient from 100%
Millipore water to 100% 1M NH4HC03, collect and pool
appropriate fraction and isolate by freeze drying. Dissolve
the product in a 100 mM solution of triethylamine ammonium
acetate (TEAA) (1 ml) and apply to a Reversed Phase HPLC (C18)
with a linear gradient from 100% 100 mM TEAA to 50% 100 mM
TEAR / 50% 100 mM TEAA/acetonitrile (1/1 v/v), collect and
pool the appropriate fraction and remove solvents by repeated
evaporation in vacuo. Pass the product overa cation exchanger
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(Dowex) in the lithium form, isolate the product by freeze
drying.
5
Dissolve [Pt(en)(BioDadoo-NH2)(N03)](N03) (6 mg, 0.008 mmol) in
2 ml of Millipore water. Add 2'-deoxyuridine-5-aminoallyl-5'-
triphosphate (2 mg, 0.004 mmol) and adjust the pH to 8.
Incubate for 24 hours at 50°C, freeze-dry and redissolve in
10 Millipore water (1 ml) and filter through a membrane filter.
Apply the mixture to a FPLC with MonoQ and purify with a
linear gradient from 100 Millipore water to 100 1M NH4HC03,
collect and pool appropriate fraction and isolate by freeze
drying. Dissolve the product in a 100 mM solution of
15 triethylamine ammonium acetate (TEAR) (1 ml) and apply to a
Reversed Phase HPLC (C18) with a linear gradient from 100 100
mM TEAA to 50~ 100 mM TEAA / 50~ 100 mM TEAA/acetonitrile (1/1
v/v), collect and pool the appropriate fraction and remove
solvents by repeated evaporation in vacuo. Pass the product
overa cation exchanger (Dowex) in the lithium form, isolate
the product by freeze drying.
Example 4
B"pa~'ri tam for coub~ ~ ncx Pt( en1 -combounds to DNA
Typical reaction fox labeling DNA molecules with a Pt-
compound according to the invention.
5 ~.g of double stranded DNA is sonicated or DNase treated to
yield fragments of 300-500 bp. 6 ~.g of Pt(en)-compound is
added and the volume is adjusted to 50 ~.1 with demineralised
water. The reaction mixture is incubated at 65°C for 1 hour.
Non-bound Pt(en)-compound is blocked by adding 100 ~,1 of a
NADDTC solution. The Pt(en)-compound labeled DNA is purified
on a sphadex G-50 column. Readily labeled and purified DNA is
stored at -20°C or used directly in a DNA probe based assay.
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Pt(en)-compound labeled DNA probes can be stored at least 2
years at -20°C without loss of activity and/or specificity.
All applications mentioned are carried out with probes labeled
according to this protocol.
Example 5
Biotin labeling of DNA probes with [Pt(en)(BioDadoo-
NHZ)(N03)](N03) (BioDadoo-ULS).
Introduction
The labeling method has been used to label DNA probes with
Biotin for In Situ Hybridization (ISH). In this example
labeling procedures including the protocols and data for
quality control procedures are presented. For Biotin labeling
a plasmid cloned total DNA of Human Papilloma Virus type 6
(HPV-6, 40~ GC basepairs) was used.
Experimental procedures
Plasmid DNA preparation
Total DNA of Human Papilloma Virus type 6 was cloned into
vector pSp-64. Plasmid DNA was transferred into E.coli (C-600)
and plated onto ampicillin containing LB plates Single
colonies were grown overnight in large culture.
Plasmid DNA was isolated according to the method of Birnboim
and Dolyl, purified by Sepharose C1-2B columnchromatography
(Pharmacia) and checked for inserts by restriction-enzyme-
analyses. Plasmid DNA concentration was determined by A260/280
absorbtion. After ethanol precipitation the DNA was
reconstituted in lOmM TRIS/HC1 pH 7.2, 0.3mM EDTA to a final
concentration of 1 ~.g/~.l (batch# 150894). Subsequently this
DNA was sonicated (Soniprep 150., MSE) for 3 times 10 minutes
(amplitude 5 microns) on ice.
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The size of the resulting DNA fragments was determined by 2%
agarose gel electrophoresis and found to be in between 200-400
basepairs (batch# 051094).
Plasmid DNA labeling and purification
Plasmid HPV-6 DNA was labeled with BioDadoo-ULS by mixing the
following reagents:
plasmid HPV-6 DNA (batch# 051094) 5 E1.1 (1 ~..l.g/~.~.1)
BioDadoo-ULS labeling reagent 8 ~,1 ( 1 ~.g/~.1 )
(batch# BX940830)
Demineralised water ( <0 . 2/ ~S/cm) 37 E.t,l
The 50 ~1 reaction mixture was incubated for 15 minutes at
85°C .
Excess of labeling reagent was captured by adding 50 ~.1 sodium
diethyldithiocarbamate (2~ solution in demineralised water)
and incubating for 30 minutes at room temperature.
Unbound BioDadoo-ULS was removed, using a S300 HR microspin
column (Pharmacia), by size exclusion chromatography.
Eluent volume was adapted to 500 ~l giving a 10 ng/~.l biotin
HPV-6 probe concentration (batch# 061094).
Quality control for detection limits
The detection limit of the biotin probe of the invention was
determined by direct spot blot and reversed
filterhybridization according to the following protocols:
Direct spot blot
HPV-6 probe (batch# 061094) labeled with biotin according to
the invention was 10-fold serially diluted into spot buffer
comprising 900mM sodium chloride, 90mM sodium citrate and 200
~g/ml single stranded salmon sperm DNA giving a dilution
series varying from 1000-0.1 pg biotin probe per ~.1.
1 ~1 spots were applied onto nitrocellulose membrane and
incubated for 2 hours at 80°C to bind the DNA. The biotin
probe was visualized using a streptavidin-alkaline phosphatase
conjugate (Sigma) combined with a NBT/BCIP precipitating
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substrate solution (Sigma) according to the following
protocol:
- Membranes were soaked in TBS solution containing 0.5~
tween20 (TBST) for 5 minutes.
- Membranes were incubated with Strep-AP (3 DEA U/ml) in TBST
for 15 minutes at 37°C.
NC-membranes were washed 3 times 5 minutes in TBS solution
followed by a 5 minute wash step in demineralised water.
- Membranes were incubated with NBT/BCIP substrate solution
for 15 minutes at 37°C, subsequently washed in demineralised
water and air dried.
Results
By using this method the detection limit of the biotin DNA
probe according to the invention was found to be less than 1
Pg
Reversed filterhybridization
HPV-6 DNA (batch# 051094) wasl in 10 diluted in O.1N NaOH,
incubated at 100°C for 5 minutes and directly placed on ice
for 5 minutes to make DNA single stranded.
A 10-fold serial dilution was made in cold 0.1N NaOH to give a
series varying from 10,000-lpg DNA per ~1. 1 ~,1 spots were
applied onto Nylon membrane (Boehringer Mannheim) and air
dried.
HPV-6 DNA probe that was labeled with biotin according to the
invention was diluted in 5xSSPE 0.5°s SDS solution to yield a
concentration of 200 ng/ml.
This sloution was incubated for 5 minutes at 100°C and placed
directly on ice for 5 minutes.
Nylon membranes containing target DNA were soaked in 2x SSC
for 5 minutes and subsequently incubated with the single
stranded probe solution for 2 hours at 37°C.
Excess of the biotin probe was removed by three changes in 2x
SSPE 0.1~ SDS for 10 minutes at 37°C followed by a 5 minutes
TBST incubation.
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The biotin probe of the invention was visualized by performing
the same protocol as described in the direct spot blot method.
Results
5 By using this procedure the detection limit of the biotin
probe according to the invention was found to be less than 10
Pg
Performance in In Situ Hybridization
10 The test material consisted of 6 Eun paraffin sections of a
HPV-6 posotive cervical condyloma mounted on organosilane
coated glass slides.
The following protocol was applied (unless otherwise stated
steps are at room temperature):
15 1 Paraffin sections were dewaxed in 3 changes of xylene and
hydrated in graded ethanol.
2 Sections were rinsed in TBST for 5 minutes.
3 Sections were digested in 0.25% pepsin in O.1N HCl for 30
minutes at 37°C, dehydrated in graded ethanol and air dried.
20 4 10 ~.l of probe solution was applied to a section and
covered with a coverslip.
Probe solution consisted of biotin HPV-6 probe DNA labeled
according to the invention (batch# 061094) in a concentration
of 2 ng/~.l dissolved in hybridization mixture comprising 0.6M
NaCl, 0.06M sodium citrate, 35% formamid, 10% dextransulphate,
2,5x Denhardts and 10 ~.g/ml single stranded salmon sperm DNA.
5 Slides were placed on a hot plate set at 95°C for 5
minutes to denature probe and target DNA simultaneously.
6 Hybridization was performed by placing the slides in a
humidified chamber at 37°C for 2 hours.
7 Coverslips were removed and slides were washed in 3
changes of lSmM NaCl, l.5mM sodium citrate and 5~ formamid for
10 minutes at 37°C.
8 Slides were rinsed in TBST.
9 Sections were incubated with Streptavidin AP copnjugate
(3DEA U/ml in TEST) for 15 minutes at 37°C.
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Slides were washed in TBST (3x) and demineralised water
(lx) for 5 minutes.
11 Sections were incubated with NBT/BCIP substrated solution
for 15 minutes at 37°C.
5 12 Slides were washed in demineralised water (3x) for 1
minute and sections were mounted in glycerol/gelatin.
Results
By using the sections showed blue/purple precipitates at the
10 sites of HPV-6 infected cells and minor background in the
remaining tissue.
Conclusions
The results demonstrate that DNA labeled according to the
invention has good detection limits. The present method is
very well suited for research, routine and for industrial
production of labeled nucleic acids, as the method is fast and
easy to perform, very sensitive, and does not include any
enzymaic step, which makes it highly reproducible and fitted
for an overall low cost production. The method of the
invention offers a useful alternative equaling conventional
non-isotopic labeling methods.
General references
1. Maniatis T., Sambrook J., Fritsch E.F., Molecular Cloning,
Second Edition, Cold Spring Harbor Laboratory Press, ISBN 0-
8769-309-6.
2. Keller G.H., Manak M.M., DNA probes, Stockton Press, ISBN
0-333-47659-X.
1. The use of Pt-DNA linkers of the invention in the so
called LIDIA technique: Linked DNA immuno Assay.
The LIDIA technique enables the quantitative analysis of
small amounts of DNA (or RNA) e.g. after a PCR amplification
of the starting material. The technique is sensitive and
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specific, due to the use of specific DNA(RNA) probes in
accordance with the invention and easy to perform, because of
the quick DNA(RNA) Pt-labeling steps of the invention.
Description of the technique:
The technique uses fast Pt labeling compounds of the invention
to label DNA(RNA) probes
This technique is possible with 3 different approaches.
1. Linking DNA probes molecules to a surface by using a Pt
compound in accordance with the invention which cross-link
DNA molecules irreversibly to plastic, nylon or
nitrocellulose. Detection of DNA targets can then be
accomplished by using classically labeled DNA/RNA
probes.(nick translation or chemical modification, random
priming)
2. Linking a detectable group to the DNA, to render a DNA
molecule into a so-called DNA probe. Binding of DNA
compounds to a surface can then be accomplished by using
classic techniques known to science (covalent linking to
specially treated microtiter plates, baking of DNA
molecules onto nitrocellulose or binding of DNA molecules
to nylon membranes.
3. A combination of techniques 1 and 2
Approach 1
An immobilized DNA probe can be used to catch specific
target molecules in a sample by using a hybridization
technique. Detection of formed hybrids can be done by using
different techniques, e.g. a second labeled DNA probe can be
used to hybridize with a different site on the target DNA
molecule to form a sandwich hybrid. The label can then be
detected by using state of the art immunological detection and
colouring techniques.
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Approach 2
A volume containing (amplified) detectable DNA(RNA) is
directly labeled according to the protocol in accordance with
the invention.
Excess label is quenched by adding NaDDTC or Thioureum.
This approach distinguishes itself from other techniques by
the fact that the target molecule is labeled in contrast to
other assay were labeled DNA(RNA) probes are used to detect
the target. The quick binding capacity of the Pt-label
compound of the invention enables a DNA binding step as a
routine step in a diagnostic test procedure (normal binding
times are 60 minutes at 65°C).
A second step is performed in a microtiter plate
precoated with a target specific probe. Incubation is allowed
to the formation of stable "Labelled target" and probe
hybrids. The direct labeling of target molecules enables the
omission of laborious double hybridization techniques where
one probe is used to catch the target and another labeled
probe is used to detect the immobilized target.
In this method the probes are covalently linked to the
microtiter plate to the surface of the wells. The second
incubation step has the character of a liquid hybridisation
and therefore can be performed very rapidly. This is one of
the main innovative features of this approach to quantitive
DNA hybridisation techniques.
Approach 3
Both for the immobilization of DNA probes or DNA targets
and for the labeling of DNA probes and targets the newly
developed Pt system can be used. These two DNA linking
techniques can be combined into one assay where both the
"catcher" and the "detector" are linked to a second substance
(either a detectable group like biotin, digoxigenin or a
carrier surface like a plastic stick, microtiter plate or a
membrane).
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Examples of the technique: the detection of STD related
microorganisms in human diagnostics (Chlamydia, Syfilis, AIDS,
Herpes, Gonorrhoea, Hep. B,)
2. The use of Pt-DNA labels .of the invention in
combination with test strip procedures and formats.
The "DNA Dipstick".
The DNA dipstick technique enables the qualitative and
semi-quantitative analysis of small amounts of DNA(or RNA)
e.g. after a PCR amplification or freely present in samples of
body fluids (blood, urine, sweat etc.)
The technique is sensitive and specific, due to the use
of specific DNA(RNA) probes and easy to perform because of the
quick DNA(RNA) Pt-labeling steps according to the invention.
The universal labeling characteristics of the newly
developed Pt label can be used in 3 ways to achieve a bound
DNA(RNA) molecule.
1. It can be used to attach a detectable marker group to a
polynucleotide sequence.
2. It can be used to attach polynucleotide sequences
irreversibly to a solid phase (plastic, membranes, latex
beads, hydrosols or microtiter plate wells).
3. A combination of 1 and 2
ad 1:
In this example there is a twofold approach to the
detection of biolytes biological analytes in test samples.
Firstly a DNA probe can be labeled with the newly developed Pt
labeling compound. This labeled probe can then be used to
detect preformed hybrids on a membrane formed between the
target DNA sequence and a primary probe. It is essential in
this method that the primary probe recognizes a different
sequence on the target than the secondary Pt labeled probe. In
practice, this can be achieved for instance with RNA
hybridization were a POLY A probe is used as a primary probe
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to immobilize all RNA (recognizable by its polyT tails) to a
membrane.
The second approach differs slightly in that in this case
the target can be labeled in the test sample fluid, because of
5 the fast and very specific Pt labeling characteristics. A
procedure like this would comprise a catch of the labeled
target with an immobilized specific unlabeled DNA probe on a
suitable membrane. Hence a dipstick version for DNA/RNA
applications.
ad 2:
To immobilize DNA probes or target DNA, a non-labeled Pt
compound (that is a Pt compound with 2 free binding sites) can
be used to act as a bridge between DNA and the surface of
carriers (plastic, membrane, microtiter plates etc.)
It greatly enhances the usability of DNA sequences as
catcher molecules in diagnostic assays, since there are little
substances known to science that bind readily DNA in a
spontaneous way. Introducing this Pt bridge molecule a wide
field of new applications for the DNA technology has come
within reach.
ad 3: a combination of example 1 and 2
General: the use of the Pt compound of the invention in
latex or hydrosol assays is particularly interesting. The
compound enables the coupling of DNA molecules to small
particles. The DNA molecules can be hybridized to target
material. A positive reaction is visualized by an
agglutination of the particles, due to crosslinking of the DNA
hybrid particle compounds.
A test like this can be made quantative, the rate of
agglutination can be tuned and measured at a specific
wavelength. Especially gold particles have the intrinsic
characteristic that a shift in optimal wavelength occurs after
agglutination.
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3. Detection of Platinated DNA probes of the invention
with the the silver-enhancement technique.
Platinated DNA/RNA probe can be employed in hybridisation
methods to detect DNA/RNA sequences in sample material. The
introduction of a platinum compound at the site of the target
enables the deposition of Ag molecules in a chemical reaction
especially designed to reduce ionic silver to metallic silver.
At the site of a Pt nucleus a decomposition of metallic
silver(black) occurs due to the catalytic effect of the Pt
nucleus.
Ionic silver is reduced by a reducing agent (e. g.
Na-borohydrid, Hydrochinon) in solution. In a constant ratio
the amount of silver deposited on the Pt is proportional to
the length of the enhancement incubation.
Visualisation of a non-visible Pt nucleus can be accomplished
by the empirical observation of the appearace of a black spot
in the test sample.
The black spots indicate the site of specific probes
binding and thus the site of specific target location.
The technique enables a quick and easy diagnostic procedure
for the detection of various microorganisms and gene
translocations/abnormalities.
